In the eastern half of the country (sites SoUt32-SoTi69), 60 Pocillopora spp. colonies were sampled (SoPd66-125). Unfortunately, I temporarily lost samples SoPd118-125 and so nucleic acids were never extracted from them. I have since found these samples, so I hope to analyze them in the future.

This presumed P. acuta colony was not analyzed due to having used these damned Direct-zol columns, which get clogged with coral skeleton. As such, I have no RNA or DNA for this biopsy. Other data can be found here:

SoPd67

This P. acuta colony was genotyped though not analyzed in full on account of a failed RNA extraction (due to using Direct-zol columns). Other data can be found here:

SoUt33: night dive site. Tagged eight Pocillopora sp. colonies (SoPd69-76) and sampled during both day and night. Despite its P. acuta-like appearance, SoPd72 was genotyped as P. brevicornis. Did not sample Seriatopora spp.

SoPd69

This P. acuta colony was sampled in both day and night, though the night sample was lost, and the RNA extraction for the day sample failed. Other data can be found here.

SoPd70

This P. acuta colony was tagged, sampled in both day and night, genotyped, and analyzed in full. The colony demonstrated aberrant behavior at night only (high RNA/DNA ratio) and was therefore considered an outlier:

This P. acuta colony was tagged, sampled in both day and night, genotyped, analyzed in full, and found to be displaying aberrant behavior during both day and not (abnormally high GFP-like chromoprotein mRNA expression in the coral host at both times). It was therefore flagged as an outlier:

Lost whole-colony image. This P. acuta colony was strange in that clade A (Symbiodinium) dinoflagellates were only detected in the daytime biopsy; the night time biopsy’s dinoflagellate community was exclusively Cladocopium (clade C). Otherwise, the colony’s behavior was statistically normal:

This P. acuta colony was tagged, sampled in both day and night, genotyped, yet the night biopsy was lost, and RNAs were not extracted from the daytime biopsy. Other data can be found here: supplemental data (JMP)

Nucleic acids were not extracted from this sample. Other data can be found here.

2014-11-15: did not dive at sites SoVa49-51.

Instead returned to SoVa47 for two additional dives since there were so many Pocillopora spp. colonies there displaying aberrant coloration (SoPd101-104). Only sampled one Seriatopora sp. colony (SoSe148) during the latter of these two dives (SoVa47-round 3).

SoPd101

Both normally and abnormally pigmented sections of this P. acuta colony were sampled. Neither portion was found to be displaying aberrant behavior, though:

Both normally and abnormally pigmented sections of this P. acuta colony were sampled, and, strangely enough, the normally pigmented biopsy had such a high dinoflagellate density as to warrant its labeling as an outlier:

This P. acuta colony was tagged, sampled in both day and night, genotyped, and analyzed in full; the night time biopsy was found to be displaying aberrant behavior (predominantly due to an abnormally high RNA/DNA ratio):

This P. acuta colony was tagged, sampled in both day and night, genotyped, and analyzed in full. Interestingly, the dinoflagellate assemblage differed over time; clade D cells were only detected in the daytime biopsy, not in the night time one. This could be due to having sampled from a different part of the colony (not related to time).

This presumed P. acuta colony was not analyzed in full due to a failed DNA extraction. Other data can be found here.

SoPd113-outlier

Both normally pigmented and bleached portions of this P. acuta colony were sampled, and the healthy biopsy was characterized by aberrant GFP-like chromoprotein gene expression; the sample was consequently delineated as an outlier.

Both normally pigmented and bleached portions of this P. acuta colony were sampled. Unfortunately, the RNA spike assay performed poorly with one of the two biopsies; it was thus removed from the dataset and not considered in the statistical analysis. I am uploading data, but please realize that the aberrant values are likely methodological in nature (and not necessarily because the coral itself was behaving strangely).

Both normally and abnormally pigmented biopsies were sampled from this presumed P. acuta colony. I hope to analyze them in the future. Other data can be found here.

SoRi60: sampled three Pocillopora spp. colonies (SoPd119-121) only. These samples got mixed up in the Palau samples box and so were never extracted, but I hope to get to them in the future. For these samples, as well as SoPd101-104, SoPd113-115, and SoPd117-119, I sampled both a normally pigmented biopsy and an abnormally pigmented one (bleached, in some cases) from the same colony to look at intra-colony differences.

SoPd119 normal vs. abnormal

Both normally and abnormally pigmented biopsies were removed from this presumed P. acuta colony, though neither was processed due to having temporarily misplaced the tubes. I aim to get back to these in the future. Otherwise, supplemental data about the colony can be found here.

SoPd120 normal vs. abnormal

Nucleic acids have not yet been extracted from the normally and abnormally pigmented biopsies taken from this sample. Other data can be found here.

SoPd121

Sampled both normally and abnormally pigmented sections of this presumed P. acuta colony. Nucleic acids have not yet been extracted. Other data can be found here.

Reef Islands day 4: 2014-11-20 (SoRi61-63 and SoRi56-round 2)

SoRi61-62: did not dive. Instead, I returned to site SoRi56 to sample more Seriatopora spp. colonies (n=7: SoSe183-189).